Chris Rhodes Week 14: Difference between revisions

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==Increased GO Terms==
==Increased GO Terms==
#RNA metabolic process:
#RNA metabolic process: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0016070&session_id=4661amigo1323124097 AmiGO Link]
#regulation of transcription:
#regulation of transcription: Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0006355 AmiGO Link]
#regulation of nitrogen compound metabolic process:
#regulation of nitrogen compound metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0051171&session_id=5368amigo1323124345 AmiGO Link]
#regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process:
#regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process: Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0019219&session_id=9876amigo1323124438 AmiGO Link]
#regulation of macromolecule biosynthetic process:
#regulation of macromolecule biosynthetic process: Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0010556&session_id=1226amigo1323124542 AmiGO Link]
#regulation of gene expression:
#regulation of gene expression: Any process that modulates the frequency, rate or extent of gene expression. This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0010468&session_id=6163amigo1323124600 AmiGO Link] 
#regulation of cellular macromolecule biosynthetic process:
#regulation of cellular macromolecule biosynthetic process: Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:2000112&session_id=490amigo1323124678 AmiGO Link]
#regulation of cellular biosynthetic process:
#regulation of cellular biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0031326&session_id=7064amigo1323124805 AmiGO Link]
#regulation of biosynthetic process:
#regulation of biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0009889&session_id=3245amigo1323124873 AmiGO Link]
#regulation of macromolecule metabolic process:  
#regulation of macromolecule metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. [http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0060255&session_id=6216amigo1323124944 AmiGO Link]


==Top Ten Regulated Genes==
==Top Ten Regulated Genes==

Revision as of 15:43, 5 December 2011

Files

Calculations XLS

GenMapp TXT

Increased MAPPFinder Results XLS

Decreased MAPPFinder Results XLS

Increased MAPPFinder Results TXT

Decreased MAPPFinder Results TXT

Materials we need

  • Table of significant genes at p< 0.05,0.01,0.001
  • Top ten significant genes
  • Top ten increased/decreased GO terms
  • Make a list of the functions of the top ten genes.
  • Take all of this data and hypothesize why under the conditions of the experiment they would be up or down regulated.
  • How do your top ten significant genes relate to the GO terms? How do they relate to the experimental conditions?
  • How do your results and hypothesis align with the paper you read?

Decreased GO Terms

  1. fructuronate reductase activity: Catalysis of the reaction: D-mannonate + NAD(+) = D-fructuronate + H(+) + NADH AmiGO Link
  2. precorrin-3B C17-methyltransferase activity: Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-3B = S-adenosyl-L-homocysteine + precorrin AmiGO Link
  3. precorrin-2 C20-methyltransferase activity:Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-2 = S-adenosyl-L-homocysteine + H(+) + precorrin-3A AmiGO Link
  4. coniferyl-aldehyde dehydrogenase activity: Catalysis of the reaction: coniferyl aldehyde + H2O + NAD(P)+ = ferulate + NAD(P)H + H+ AmiGO Link
  5. inositol-1(or 4)-monophosphatase activity: Catalysis of the reaction: myo-inositol phosphate + H2O = myo-inositol + phosphate AmiGO Link
  6. trans-2-enoyl-CoA reductase (NADPH) activity: Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+ AmiGO Link
  7. aldehyde dehydrogenase [NAD(P)+] activity: Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+ AmiGO Link
  8. oxidoreductase activity:The catalysis of redox reactions specifically relating to energy functions such as NAD+/NADH AmiGO Link
  9. inositol or phosphatidylinositol phosphatase activity: Catalysis of the reaction: inositol phosphate(n) + H2O = inositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from an inositol phosphate AmiGO Link
  10. cellular aldehyde metabolic process: The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells AmiGO Link

Increased GO Terms

  1. RNA metabolic process: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage AmiGO Link
  2. regulation of transcription: Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription AmiGO Link
  3. regulation of nitrogen compound metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds AmiGO Link
  4. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process: Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids AmiGO Link
  5. regulation of macromolecule biosynthetic process: Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. AmiGO Link
  6. regulation of gene expression: Any process that modulates the frequency, rate or extent of gene expression. This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein AmiGO Link
  7. regulation of cellular macromolecule biosynthetic process: Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process AmiGO Link
  8. regulation of cellular biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells AmiGO Link
  9. regulation of biosynthetic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances AmiGO Link
  10. regulation of macromolecule metabolic process: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. AmiGO Link

Top Ten Regulated Genes

Links

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